The Stanford Microarray Database (SMD) is an open source, DNA microarray research database, which can support the research needs of single laboratories, collaborating groups, all the way up to being an institutional- scale database, serving thousands of users at many locations. As a research database system, SMD provides not only data storage and access control, but current biological annotation and a variety of tools for data retrieval, quality assessment and analysis, which support pre- and post-publication uses of microarray data. SMD supports both two-color data (including the output of the GenePix, ScanAlyze, and Agilent feature extraction software) and single-channel data from Affymetrix GeneChips and Nimblegen Arrays. The Stanford installation serves hundreds of researchers at Stanford and their collaborators at over one hundred institutions worldwide, and provides public access to data from approximately 12,000 microarrays. SMD's software has had regular releases over the last three years, and been installed at several other institutions on a variety of operating systems and database platforms, serving many researchers at those sites. The major goals of this proposed project are to expand and improve the tools in SMD to further enable biomedical research, and to provide biologists and data analysts with greater control and consistency in their analyses. In the first funding period of this grant, we specifically focused on development of the database infrastructure to make robust and regular releases of SMD's code and schema. In this renewal application, we are expanding our focus to provide additional tools that will benefit users of SMD installations. Specifically, we propose to (1) provide continued maintenance, release and support of the SMD software package, (2) significantly increase the number of analysis tools and speed with which they can be adopted by integrating the GenePattern software into the SMD software package, which will also allow users to create data retrieval pipelines, (3) create tools that enable SMD users to easily import data from the ArrayExpress and GEO public microarray data repositories and (4) provide data structures and software to provide support in SMD for higher density platforms, such as tiling and SNP arrays. In sum, completion of these aims will provide biomedical researchers and clinicians with powerful tools that will allow them to more completely analyze their own microarray data, as well as derive more benefit from already published microarray data, thereby increasing the value of both. Biomedical research is rapidly evolving, largely due to the application of high-throughput technologies, such as microarrays. Many clinicians and researchers are using microarrays in innovative ways to investigate a diversity of human diseases, from cancer to infectious diseases to heart disease, as well as fundamental aspects of basic biology, which frequently provide new insights into human biology. This proposal provides these researchers with a database and tools with which they can organize and analyze their data, and ensure that their research has the greatest possible impact on human health.